Lp_0172 phylogeny, gene context and selected regions
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lp_0172 phylogeny, gene context and selected regions. selected regions. group 3 in N-term tree. lp_0172. lsl_1283. lms_0142. lru_1170. lbe_0363. pep_0537. orthologous cluster: lp_1729/ lp_1730/ lp_1731. lp_0173 phylogeny, gene context and selected regions. selected regions. lp_0175.

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lp_0172 phylogeny, gene context and selected regions

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Lp 0172 phylogeny gene context and selected regions

lp_0172 phylogeny, gene context and selected regions

selected regions

group 3 in N-term tree

lp_0172

lsl_1283

lms_0142

lru_1170

lbe_0363

pep_0537

orthologous cluster:

lp_1729/ lp_1730/ lp_1731


Lp 0172 phylogeny gene context and selected regions

lp_0173 phylogeny, gene context and selected regions

selected regions

lp_0175

lp_0173


Lp 0172 phylogeny gene context and selected regions

lp_0188 phylogeny, gene context and selected regions

selected regions


Lp 0172 phylogeny gene context and selected regions

lp_2256 CcpA gene context and selected regions

selected regions

selected the Lactobacilli and Leuconostoc mesenteroides


Lp 0172 phylogeny gene context and selected regions

lp_2602 phylogeny, gene context and selected regions

selected regions

hydrolase


Lp 0172 phylogeny gene context and selected regions

lp_3221 phylogeny, gene context and selected regions

selected regions

3221

3223

1604

LSE

1606

1604


Lp 0172 phylogeny gene context and selected regions

lp_3531 and lp_3625 phylogeny, gene context and selected regions

laci_selected_onestraineach.jpeg

selected regions

upstream regions chosen on basis of similarity of motif


Lp 0172 phylogeny gene context and selected regions

selected regions

lp_3661 phylogeny, gene context and selected regions

ORF calling

laci_selected_onestraineach.jpeg


Lp 0172 phylogeny gene context and selected regions

phylogeny of lp_3470 (lacR), lp_3479 and lp_3488 from L. plantarum

lp_3470

B

A

lp_3479

lp_3488


Lp 0172 phylogeny gene context and selected regions

lp_3470 gene context and selected regions

selected regions

A

3469

3470

A

3412

A

0829

0828

B

1379

1376

1378

B

0857

0855

0856

B

1388

1387

0350


Lp 0172 phylogeny gene context and selected regions

selected regions

Lp_3479 gene context and selected regions

3479

OOE 1093

LBE 1856

MN 1418

PN 0747

SPR 1831

LRE 1261

LCA 0407 and LSE 0407

0380

0764

STH 0744


Lp 0172 phylogeny gene context and selected regions

selected regions

Lp_3488 gene context and selected regions

3485

3488

3487

3486

L. plant (LPL)

0412

0413

1517

P. pent (PEP)


Lp 0172 phylogeny gene context and selected regions

Selected upstream sites to create TF-specific binding motifs

172

>LSL01282-Lactobacillussalivariussubsp.salivariusUCC118(IG-157),NC_007929_1322719_1321367

ATCGCAAACGGTTGCAAA

>PEP00536-PediococcuspentosaceusATCC25745,NC_008525_974542_973202

AGTGCAAACGCTTGCACA

>LBE00365-LactobacillusbrevisATCC367,NC_008497_381212_382582

TGCGCAATCGGTTGCATT

>LPL01729-LactobacillusplantarumWCFS1,LPL_1565021_1566364

CACGCAAACGCTTGCATA

>LMS00144-LeuconostocmesenteroidesATCC8293,NC_008531_891162_892511

CGGGCAAACGCTTCCAAA

173

>LPL00175-LactobacillusplantarumWCFS1,LPL_151222_152472

TCTGTTAACGTTAACATT

>LMO02124-ListeriamonocytogenesEGD-e,NC_003210_2208362_2207106

CTTGTAAACGCTTTCGAA

>BS03456-Bacillussubtilis168,BACSU_3554836_3553586

TCTGTTATCGGTAACAAA

>BLH00606-BacilluslicheniformisDSM13,NC_006322_662015_663265

TCTGTTACCGGTAACAGG

188

>LPL00187-LactobacillusplantarumWCFS1,LPL_167690_169192

ATGTCAAACGATTGACAT

>PEP01800-PediococcuspentosaceusATCC25745,NC_008525_574186_575688

ATGTCAAACGATTGACAT

>EF00492-EnterococcusfaecalisV583,NC_004668_1557238_1558695

ATGTTATACGTTTGACTT

>SAG01646-Streptococcusagalactiae2603V/R,NC_004116_1691408_1692844

ATGTCAAGCGTTTGACAT

>SPM01882-StreptococcuspyogenesM18MGAS8232,NC_003485_1562572_1564008

ATGTCAAGCGTTTAACAT

>MN00134-StreptococcusmutansUA159,Contig2_1741398_1742834

ATGTCAATCGTTTTACAT

>LSK01793-Lactobacillussakeisubsp.sakei23K,CR936503_1779379_1780851

ATGTCAAACGATTATCAT

>LSL00065-Lactobacillussalivariussubsp.salivariusUCC118(IG-157),NC_007929_81998_80511

ATGTTATACGATTGACAG

>LAC00383-LactobacillusacidophilusNCFM,NC_006814_375108_373654

ATGTCAATCGTTTGACAC

>LJO00518-LactobacillusjohnsoniiNCC533,NC_005362_1861776_1863242

ATGTCAAGCGCTTATCAT

>LGA00093-LactobacillusgasseriATCC-33323(JGI),NC_008530_1764253_1765719

ATGTCAAGCGCTTATCAC

>STH00541-StreptococcusthermophilusCNRZ1066(IG-40),NC_006449_1552093_1553532

ATGTCAAACGTTTAGCAT

2256

>LPL02256-LactobacillusplantarumWCFS1,LPL_2040324_2039317

CATGAAAGCGATTTCAAT

>LBE01171-LactobacillusbrevisATCC367,NC_008497_1178074_1177076

TTCGAAAACGTTTTCAAT

>LSE00755-LactobacilluscaseiATCC334,NC_008526_804301_805299

CAGTAAAACGCTTGCATT

>LSL00420-Lactobacillussalivariussubsp.salivariusUCC118(IG-157),NC_007929_463530_464534

TTATGAAACGCTTGCAAT

>LME00420-LeuconostocmesenteroidesATCC-8293(JGI),scaffold_19_12466_11462

GTTGTAAGCGTTTGCAAT

>LDB00875-Lactobacillusdelbrueckiisubsp.bulgaricusATCC11842(IG-98),NC_008054_1368486_1367488

GCTGTAAGCGATTGCACC

>LJO00491-LactobacillusjohnsoniiNCC533,NC_005362_545423_546415

GTCGTAAACGGTTGCAAT

>LGA00804-LactobacillusgasseriATCC-33323(JGI),NC_008530_462533_463570

GTCGTAAACGGTTGCAAT

>LAC00414-LactobacillusacidophilusNCFM,NC_006814_405409_406407

GCTGTAAACGTTTGCAAT

>PPE01697-PediococcuspentosaceusATCC25745(JGI),scaffold_9_21906_20905

TTTGATAACGTATTCATG

2602

>LPL02602-LactobacillusplantarumWCFS1,LPL_2322719_2321784

CCTGGTACCGGTTTCACA

>SAG00762-Streptococcusagalactiae2603V/R,NC_004116_781580_782386

CATGGAACGGGTTCCAGC

>LSK01554-Lactobacillussakeisubsp.sakei23K,CR936503_1526189_1527010

CCTGGGACGCGTTTCATA

3221

>LPL03221-LactobacillusplantarumWCFS1,LPL_2871483_2870485

TATGGAAACGATTCCAAA

>LSE01604-LactobacilluscaseiATCC334,NC_008526_2095700_2094702

AATGAAATCGATTCCATA

3531

>LPL03533_1-LactobacillusplantarumWCFS1,LPL_3150332_3151750

AGTGTAAACGTTTACTTT

>LPL03533_2-LactobacillusplantarumWCFS1,LPL_3150332_3151750

ATTGTAAACGTTTACGTT

>OON00187_1-OenococcusoeniPSU-1,NC_008528_40575_39163

ACAGTAAACGTTTACTAT

>OON00187_2-OenococcusoeniPSU-1,NC_008528_40575_39163

ATTGTAAACGTTTACTGT

>OON00187_3-OenococcusoeniPSU-1,NC_008528_40575_39163

TTTGTAAACGTTTACTTA

>LRE01125-LactobacillusreuteriJCM1112,AAOV01000033_9204_7525

TAAGTAAACGTTTACATT

>LME01514-LeuconostocmesenteroidesATCC-8293(JGI),scaffold_57_4727_6394

ATTGTAAACGTTTACGCA

3625

>LPL03627-LactobacillusplantarumWCFS1,LPL_3242794_3241121

TAAGCAAACGTTTGCTTA

>LBE02143_1-LactobacillusbrevisATCC367,NC_008497_2145014_2146393

TACACAAACGTTTGCTTT

>LBE02143_2-LactobacillusbrevisATCC367,NC_008497_2145014_2146393

ATTGCAAACGTTTGTGTA

>SHA00075-StaphylococcushaemolyticusJCSC1435,NC_007168_82213_80498

TACTCAAACGTTTGAGTA

3661

>LPL03660-LactobacillusplantarumWCFS1,LPL_3281249_3280332

TCATAAAACGTTTTAATA

>EF00346-EnterococcusfaecalisV583,NC_004668_2834340_2833432

TACTAAAACGTTTTAATT

>PEP00437-PediococcuspentosaceusATCC25745,NC_008525_1674652_1673747

TCATAAAACGTTTTAAAC

>EFA02850-EnterococcusfaeciumDO(JGI),Contig0036_2675_1746

TACTAAAACGTTTTAAAA

>LSK00196-Lactobacillussakeisubsp.sakei23K,CR936503_193092_193973

TAGTAAAACGTTTTACTA

>SAM00277-StaphylococcusaureusMu50,NC_002758_315158_314280

TGGTAAAACGTTTTACTA

3470

>LMS00828

ATCATTTACTAATTTTT

>LMS00828

TAAATTTAGTAATGAAA

>LMS00828

ACATTTGACTAATGTAA

>LPL03469

TTATTTTAGTAAAACGG

>LPL03469

GATATTTAGTAATTATT

3479

>LSE00410

TATTTTTAGTAAAATAA

>LSE00410

AATTTTTAGTAAAAGGA

>LPL03482

AAATTTTAGTAAAACTA

>LPL03482

TCGTTTTAGTTAAACTT

>OOE01095

GGAATTTAGTAAATATT

>LRE01263

TGTATTTAGTAAAAGTT

>LSK00764

AACATTTACTAAAAAAT

>LSK00765

ATTTTTTAGTAAATGTT

>LSK00764

TCATTTTACTAAACATT

>LSK00765

AATGTTTAGTAAAATGA

>LSL00381

AAAGTTTACTAAAAAGT

>LSL00380

ACTTTTTAGTAAACTTT

>LSL00381

TATTTTTAGTAAATTTT

>LSL00380

AAAATTTACTAAAAATA

>LBE01859

AAACTTTACTAAAAATT

>MN01418

AAATTTTACTAAATTTA

>MN00620

TAAATTTAGTAAAATTT

>MN01418

TATTTTTACTAAAATTT

>MN00620

AAATTTTAGTAAAAATA

>PN00747

AAATTTTAGTAAAATAT

>PN00746

ATATTTTACTAAAATTT

>PN00747

CCTTTTTACTAAAATTT

>PN00746

AAATTTTAGTAAAAAGG

>STH00745

ATATTTTACTAAAAAAA

>STH00744

TTTTTTTAGTAAAATAT

3488

>PEP01517

AAATTTTACTAAAAAAC

>PEP01517

CTAATTTACTAAAATAA

>LPL03486

AAATTTTACTAAAAATC

>PEP00412

AATATTTACTCAATCCC

>PEP00412

TATTTTAACTAAAATAT

>LPL03487

AAGTTTTACTCAACTTC

>LPL03487

TCTTTTAACTAAAAGTT


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